Biology subjects

Schroeder, R.

Publications and source records attributed to Schroeder, R..

4 recordsLinked to original sources

bioRxiv2018

Cultural Innovations influence patterns of genetic diversity in Northwestern Amazonia

Human populations often exhibit contrasting patterns of genetic diversity in the mtDNA and the non-recombining portion of the Y-chromosome (NRY), which reflect sex-specific cultural behaviors and population histories. Here, we sequenced 2.3 Mb of the NRY from 284 individuals representing more than 30 Native-American groups from Northwestern Amazonia (NWA) and compared these data to previously generated mtDNA genomes from the same groups, to investigate the impact of cultural practices on genetic diversity and gain new insights about NWA population history. Relevant cultural practices in NWA include postmarital residential rules and linguistic-exogamy, a marital practice in which men are required to marry women speaking a different language.\n\nWe identified 2,969 SNPs in the NRY sequences; only 925 SNPs were previously described. The NRY and mtDNA data showed that males and females experienced different demographic histories: the female effective population size has been larger than that of males through time, and both markers show an increase in lineage diversification beginning ~5,000 years ago, with a male-specific expansion occurring ~3,500 years ago. These dates are too recent to be associated with agriculture, therefore we propose that they reflect technological innovations and the expansion of regional trade networks documented in the archaeological evidence. Furthermore, our study provides evidence of the impact of postmarital residence rules and linguistic exogamy on genetic diversity patterns. Finally, we highlight the importance of analyzing high-resolution mtDNA and NRY sequences to reconstruct demographic history, since this can differ considerably between males and females.

genetics↗

bioRxiv2017

Contrasting maternal and paternal genetic variation of hunter-gatherer groups in Thailand

The Maniq and Mlabri are the only recorded nomadic hunter-gatherer groups in Thailand. Here, we sequenced complete mitochondrial (mt) DNA genomes and ~2.364 Mbp of non- recombining Y chromosome (NRY) to learn more about the origins of these two enigmatic populations. Both groups exhibited low genetic diversity compared to other Thai populations, and contrasting patterns of mtDNA and NRY diversity: there was greater mtDNA diversity in the Maniq than in the Mlabri, while the converse was true for the NRY. We found basal uniparental lineages in the Maniq, namely mtDNA haplogroups M21a, R21 and M17a, and NRY haplogroup K. Overall, the Maniq are genetically similar to other negrito groups in Southeast Asia. By contrast, the Mlabri haplogroups (B5a1b1 for mtDNA and O1b1a1a1b and O1b1a1a1b1a1 for the NRY) are common lineages in Southeast Asian non-negrito groups, and overall the Mlabri are genetically similar to their linguistic relatives (Htin and Khmu) and other groups from northeastern Thailand. In agreement with previous studies of the Mlabri, our results indicate that the Malbri do not directly descend from the indigenous negritos. Instead, they likely have a recent origin (within the past 1,000 years) by an extreme founder event (involving just one maternal and two paternal lineages) from an agricultural group, most likely the Htin or a closely- related group.

genetics↗

bioRxiv2017

Genome-wide identification of intrasplicing events in the human transcriptome and hints to their regulatory potential

Alternative splicing is one of the major regulators of both, transcriptome diversity and individual isoform abundance. Therefore regulation of alternative splicing is crucial and yet, due to the complexity of the human genome (23.000 genes, most of which can be alternatively spliced) diverse and multileveled. Identifying and understanding the scope and variety of splicing events is still an ongoing process. We established a novel pipeline to extract splicing events from specific RNA-sequencing datasets and identified numerous splicing events that did not span the entirety of the respective annotated intron but used intronic splice sites. These splicing events could be generally categorized into three groups: 5recursive (using the exonic splice donor and intronic acceptor), 3recursive (using an intronic splice donor and an exonic acceptor) and nested (using two intronic splice sites). Surprisingly, the splicing events we found occurred in introns of all lengths, but generally followed the abundance scheme of all introns, i.e. most were found in introns between 500 and 5000 bps. After confirmation of these splice events by conventional methodologies, we further analyzed the impact of intrasplicing on full intron removal. For this we established a luciferase-based reporter which showed that these intronic splicing steps can be beneficial, deleterious or neutral for full intron removal. Thus intrasplicing events can be crucial for determining the transcriptional output. This in part confirms recent findings on recursive splicing events in humans and other vertebrates and further uncovers an additional level of transcriptome regulation based on a yet undiscovered level of flexibility and regulation of splice site selection and its impact on gene expression.

biochemistry↗

bioRxiv2017

Mitochondrial DNA heteroplasmy is shared between human liver lobes

Mitochondrial DNA (mtDNA) heteroplasmy (intra-individual variation) varies among different human tissues and increases with age, suggesting that the majority of mtDNA heteroplasmies are acquired, rather than inherited. However, the extent to which heteroplasmic sites are shared across a tissue remains an open question. We therefore investigated heteroplasmy in two liver samples (one from each primary lobe) from 83 Europeans, sampled at autopsy. Minor allele frequencies (MAF) at heteroplasmic sites were significantly correlated between the two liver samples from an individual, with significantly more sharing of heteroplasmic sites in the control region than in the coding region. We show that this increased sharing for the control region cannot be explained by recent mutations at just a few specific heteroplasmic sites or by the possible presence of 7S DNA. Moreover, we carried out simulations to show that there is significantly more sharing than would be predicted from random genetic drift from a common progenitor cell. We also observe a significant excess of non-synonymous vs. synonymous heteroplasmies in the coding region, but significantly more sharing of synonymous heteroplasmies. These contrasting patterns for the control vs. the coding region, and for non-synonymous vs. synonymous heteroplasmies, suggest that selection plays a role in heteroplasmy sharing.

genetics↗